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52 results for “Historical DNA”
Figure 5. Per-base coverage plots for the 16S in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 5. Per-base coverage plots for the 16S fragment in four Mantidactylus type specimens from the MNHN and BMNH collections. (a) BMNH 1947.2.25.48 (paralectotype of Rana guttulata); (b) BMNH 1947.2.25.51 (paralectotype of Rana guttulata); (c) MNHN 1895.255 (syntype of M. grandidieri); (d) MNHN 1883.520 (syntype of M. grandidieri).
Figure 3 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 3. Haplotype network of the subgenus Mantidactylus based on 1227 bp of the nuclear RAG-1 gene from 39 samples. Small black dots represent additional mutational steps.
Figure 2 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 2. Diagonal matrix visualising the mean uncorrected genetic distances (p-distances) in the mitochondrial 16S rRNA gene between the different lineages in the subgenus Mantidactylus, calculated from 514 bp of the 16S mitochondrial gene.
Figure 1. Maximum likelihood phylogenetic tree obtained from 514 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 1. Maximum likelihood phylogenetic tree obtained from 514 bp of the mitochondrial 16S rRNA gene. The values at the nodes are the bootstrap supports (not given for intra-lineage nodes for improved clarity). The type specimens of M. guttulatus and M. grandidieri from the London and Paris museum collections are highlighted in red and brown, respectively.
Figure 4 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 4. Stacked barplots showing the number of reads uniquely matching different reference sequences for the three targeted mitochondrial genes with a similarity threshold of 98%. The Rana pigra type was not included because the number of reads was too low.
Figure 8 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 8. Lateral views of the heads of preserved adult males of Mantidactylus (Mantidactylus) radaka sp. nov. in comparison with M. (M.) guttulatus and M. (M.) grandidieri. Note the more distinct and larger tympanum (indicated by yellow arrows) in the latter two species. Not to scale.
Figure 6 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 6. Photographs of living specimens of Mantidactylus radaka sp. nov. (a, b) Male holotype ZSM 644/2001 (field number FGMV 2001.132) from Manarikoba forest, Tsaratanana Massif. (c–f) Female paratype ZSM 1800/2010 (ZCMV 12345) from Camp 1 (Antevialambazaha), Tsaratanana Massif. (g, h) Female paratype ZSM 97/2016 (MSZC 0080) from Ampotsidy. (i, j) Male paratype MSZC 0120 (uncatalogued in UADBA) from Ampotsidy. (k) Unidentified specimen from Camp 0 (Ankijagna Lagnana), Tsaratanana Massif. (l) Paratype ZSM 582/2014 (DRV 6073) from Camp 0 (Ankijagna Lagnana). (m, n) Unidentified female specimen from Manongarivo (Camp 0), probably preserved in UADBA collection.
FIGURE 5 in History and historical DNA: Identity of Chelodina intergularis Fry, 1915 and type localities of C. intergularis and C. rugosa Ogilby, 1890
FIGURE 5. Plastral aspects of Chelodina kuchlingi; specimens from the Western Australian Museum, Perth. From left to right: WAM R29411 (holotype), WAM R28116, WAM R28117 (some scute outlines in this specimen highlighted in blue). To scale, midline plastral length of holotype 185 mm. Note that the intergular reaches the anterior plastral rim only in the holotype. Photos: G. Kuchling.
FIGURE 4 in History and historical DNA: Identity of Chelodina intergularis Fry, 1915 and type localities of C. intergularis and C. rugosa Ogilby, 1890
FIGURE 4. Comparison of (A) the holotype of Chelodina rugosa (AM R6256), (B) the holotype of C. intergularis (AM R6255) and (C) an individual of C. burrungandjii sensu stricto (UC 2101; redrawn from Thomson et al. 2000). Not to scale. Epidermal scutes (blue): G = gular; H = humeral; I = intergular; P = pectoral. Bony plates (black): Epi = epiplastron; Ent = entoplastron; Hyo = hyoplastron. In AM R6256 the bony sutures are visible at closer inspection through the translucent epidermal scutes. Drawings: S. Thomson.
FIGURE 2 in History and historical DNA: Identity of Chelodina intergularis Fry, 1915 and type localities of C. intergularis and C. rugosa Ogilby, 1890
FIGURE 2. Maximum Likelihood tree using near-complete mitogenomes of Chelodina species, rooted with Elseya flaviventralis. Numbers at nodes are bootstrap values and posterior probabilities from a Bayesian tree of the same topology. Asterisks indicate maximum support under both approaches. Species names do not imply validity or nomenclatural availability; accepted names of terminals on the right in bold. Sequences from type specimens are flagged; that of the C. intergularis type is highlighted in red. Codes following species names are GenBank/ENA accession numbers. For specimen/voucher tissue information, see Table 1. The mitogenomic phylogeny conflicts with subgenera and reflects a complex pattern of transspecific introgression and mitochondrial capture (Hodges 2015; Kehlmaier et al. 2019).
FIGURE 1 in History and historical DNA: Identity of Chelodina intergularis Fry, 1915 and type localities of C. intergularis and C. rugosa Ogilby, 1890
FIGURE 1. Holotype of Chelodina intergularis, Australian Museum, Sydney (AM R6255). Photos: G. Shea.
Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo (DRC)
<p><span>This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1,169 bp <em>d-loop</em> region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire <em>d-loop</em> region (1,169 bp <em>d-loop</em>). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the Neighbor-joining (NJ) tree and median-joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (<em>F<sub>ST</sub></em>) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (<em>p</em>-value < 0.05) values for <em>F</em>u's <em>F</em>s (-20.418) and Tajima's (-2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long-term conservation of indigenous goats in DRC</span><span>.</span></p>
FIGURE 6. T in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 6. T-test results for morphological indicators. (F = females, M = males, N = northern Xinjiang, S = south Xinjiang)
FIGURE 5 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 5. The morphology and tail of Laudakia stoliczkana subspecies. (A & a: L. s. altaica; B & b: L. s. stoliczkana)
FIGURE 4 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 4. The estimation of divergence time for Laudakia. (Note: Values are estimated divergence times, and the blue bars are 95% confidence intervals HPD)
FIGURE 3 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 3. Bayesian phylogenetic trees of Laudakia species on tandem sequences (CO1 and 16S). (note: the values of nodes near is BPP/BS).
FIGURE 2 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 2. Bayesian phylogenetic trees of Laudakia on the sequenced of COI. (note: the values of nodes near is BPP/BS).
FIGURE 1 in Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences
FIGURE 1. Bayesian phylogenetic trees of Laudakia on the sequenced of 16S. (note: the values of nodes near is BPP/BS).
Data from: Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding
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Data from: Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA
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